LHX9.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX9.H12INVIVO.0.PS.A
Gene (human)	LHX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx9
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	bhTAATKRv
GC content	28.79%
Information content (bits; total / per base)	9.161 / 1.018
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1003

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	1 (5)	0.821	0.846	0.69	0.736	0.742	0.754	2.013	2.079	85.276	131.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.951	0.926	0.864	0.844	0.735	0.741
Overall, 8 experiments	best	0.978	0.964	0.965	0.945	0.925	0.903
Methyl HT-SELEX, 3 experiments	median	0.953	0.927	0.917	0.883	0.82	0.8
Methyl HT-SELEX, 3 experiments	best	0.964	0.944	0.943	0.914	0.877	0.851
Non-Methyl HT-SELEX, 5 experiments	median	0.948	0.925	0.811	0.805	0.649	0.681
Non-Methyl HT-SELEX, 5 experiments	best	0.978	0.964	0.965	0.945	0.925	0.903

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.932	0.597	0.905	0.557
batch 2	0.756	0.574	0.72	0.543

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HD-LIM {3.1.5} (TFClass)
TF subfamily	LHX2-like {3.1.5.3} (TFClass)
TFClass ID	TFClass: 3.1.5.3.2
HGNC	HGNC:14222
MGI	MGI:1316721
EntrezGene (human)	GeneID:56956 (SSTAR profile)
EntrezGene (mouse)	GeneID:16876 (SSTAR profile)
UniProt ID (human)	LHX9_HUMAN
UniProt ID (mouse)	LHX9_MOUSE
UniProt AC (human)	Q9NQ69 (TFClass)
UniProt AC (mouse)	Q9WUH2 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	5
Methyl-HT-SELEX	3

PCM	LHX9.H12INVIVO.0.PS.A.pcm
PWM	LHX9.H12INVIVO.0.PS.A.pwm
PFM	LHX9.H12INVIVO.0.PS.A.pfm
Alignment	LHX9.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	LHX9.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	LHX9.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	LHX9.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	LHX9.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	LHX9.H12INVIVO.0.PS.A_homer_format_0.001.txt LHX9.H12INVIVO.0.PS.A_homer_format_0.0005.txt LHX9.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	131.0	193.0	350.0	329.0
02	126.0	284.0	115.0	478.0
03	11.0	7.0	26.0	959.0
04	970.0	2.0	22.0	9.0
05	975.0	12.0	7.0	9.0
06	8.0	8.0	9.0	978.0
07	4.25	46.25	501.25	451.25
08	625.0	3.0	322.0	53.0
09	182.0	152.0	539.0	130.0

PFM

	A	C	G	T
01	0.131	0.192	0.349	0.328
02	0.126	0.283	0.115	0.477
03	0.011	0.007	0.026	0.956
04	0.967	0.002	0.022	0.009
05	0.972	0.012	0.007	0.009
06	0.008	0.008	0.009	0.975
07	0.004	0.046	0.5	0.45
08	0.623	0.003	0.321	0.053
09	0.181	0.152	0.537	0.13

PWM

	A	C	G	T
01	-0.643	-0.26	0.332	0.27
02	-0.681	0.124	-0.771	0.642
03	-2.988	-3.365	-2.209	1.336
04	1.348	-4.216	-2.365	-3.158
05	1.353	-2.912	-3.365	-3.158
06	-3.256	-3.256	-3.158	1.356
07	-3.743	-1.661	0.689	0.585
08	0.909	-3.978	0.249	-1.529
09	-0.318	-0.496	0.762	-0.651

Standard thresholds

P-value	Threshold
0.001	5.051225
0.0005	6.150595
0.0001	7.42843